Merge pull request #11 from CCBR/cutadapt

fix: modify cutadapt args for paired-end
CCBR · Oct 19, 2023 · fe697a4 · fe697a4
2 parents ae58d4f + 24a287e
commit fe697a4
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Showing 3 changed files with 22 additions and 8 deletions.
diff --git a/modules/CCBR/cutadapt/main.nf b/modules/CCBR/cutadapt/main.nf
@@ -16,15 +16,25 @@ process CUTADAPT {
         task.ext.when == null || task.ext.when
 
     script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def trimmed  = meta.single_end ? "-o ${prefix}.trim.fastq.gz" : "-o ${prefix}_1.trim.fastq.gz -p ${prefix}_2.trim.fastq.gz"
     def args = task.ext.args ?: [
             '--nextseq-trim=2',
             '--trim-n -n 5 -O 5',
             '-q 10,10',
-            '-m 20',
             '-b file:/opt2/TruSeq_and_nextera_adapters.consolidated.fa'
-        ].join(' ').trim()
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def trimmed  = meta.single_end ? "-o ${prefix}.trim.fastq.gz" : "-o ${prefix}_1.trim.fastq.gz -p ${prefix}_2.trim.fastq.gz"
+        ]
+    if (meta.single_end) {
+        args += [
+            '-m 20'
+        ]
+    } else {
+        args += [
+            '-B file:/opt2/TruSeq_and_nextera_adapters.consolidated.fa',
+            '-m 20:20',
+        ]
+    }
+    args = args.join(' ').trim()
     """
     cutadapt \\
         --cores ${task.cpus} \\

diff --git a/tests/modules/CCBR/cutadapt/nextflow.config b/tests/modules/CCBR/cutadapt/nextflow.config
@@ -2,8 +2,4 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
-    withName: CUTADAPT {
-        ext.args = '-q 25'
-    }
-
 }
diff --git a/tests/modules/CCBR/cutadapt/test.yml b/tests/modules/CCBR/cutadapt/test.yml
@@ -4,6 +4,9 @@
     - cutadapt
   files:
     - path: ./output/cutadapt/test.cutadapt.log
+      contains:
+        - "Command line parameters: --cores 2 --nextseq-trim=2 --trim-n -n 5 -O 5 -q 10,10 -b file:/opt2/TruSeq_and_nextera_adapters.consolidated.fa -m 20 -o test.trim.fastq.gz test_1.fastq.gz"
+    - path: ./output/cutadapt/versions.yml
     - path: ./output/cutadapt/test.trim.fastq.gz
 
 - name: cutadapt single-end stub
@@ -12,6 +15,7 @@
     - cutadapt
   files:
     - path: ./output/cutadapt/test.cutadapt.log
+    - path: ./output/cutadapt/versions.yml
     - path: ./output/cutadapt/test.trim.fastq.gz
 
 - name: cutadapt paired-end
@@ -20,6 +24,9 @@
     - cutadapt
   files:
     - path: ./output/cutadapt/test.cutadapt.log
+      contains:
+        - "Command line parameters: --cores 2 --nextseq-trim=2 --trim-n -n 5 -O 5 -q 10,10 -b file:/opt2/TruSeq_and_nextera_adapters.consolidated.fa -B file:/opt2/TruSeq_and_nextera_adapters.consolidated.fa -m 20:20 -o test_1.trim.fastq.gz -p test_2.trim.fastq.gz test_1.fastq.gz test_2.fastq.gz"
+    - path: ./output/cutadapt/versions.yml
     - path: ./output/cutadapt/test_1.trim.fastq.gz
     - path: ./output/cutadapt/test_2.trim.fastq.gz
 
@@ -29,5 +36,6 @@
     - cutadapt
   files:
     - path: ./output/cutadapt/test.cutadapt.log
+    - path: ./output/cutadapt/versions.yml
     - path: ./output/cutadapt/test_1.trim.fastq.gz
     - path: ./output/cutadapt/test_2.trim.fastq.gz